diff --git a/poetry.lock b/poetry.lock index 7e59ca5492e71c0eaf24276fb3a610bb0f39bc43..95e68dbae6df7d4618c146ea4c231b737ed21f47 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6,27 +6,19 @@ category = "main" optional = false python-versions = "*" -[[package]] -name = "appdirs" -version = "1.4.4" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" -optional = false -python-versions = "*" - [[package]] name = "astroid" -version = "2.4.1" +version = "2.8.5" description = "An abstract syntax tree for Python with inference support." category = "main" optional = false -python-versions = ">=3.5" +python-versions = "~=3.6" [package.dependencies] -lazy-object-proxy = ">=1.4.0,<1.5.0" -six = ">=1.12,<2.0" -typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""} -wrapt = ">=1.11,<2.0" +lazy-object-proxy = ">=1.4.0" +typed-ast = {version = ">=1.4.0,<2.0", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""} +typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} +wrapt = ">=1.11,<1.14" [[package]] name = "astunparse" @@ -63,7 +55,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "babel" -version = "2.9.0" +version = "2.9.1" description = "Internationalization utilities" category = "main" optional = false @@ -72,21 +64,39 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.dependencies] pytz = ">=2015.7" +[[package]] +name = "backports.entry-points-selectable" +version = "1.1.1" +description = "Compatibility shim providing selectable entry points for older implementations" +category = "dev" +optional = false +python-versions = ">=2.7" + +[package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} + +[package.extras] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"] + [[package]] name = "certifi" -version = "2020.12.5" +version = "2021.10.8" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = "*" [[package]] -name = "chardet" -version = "4.0.0" -description = "Universal encoding detector for Python 2 and 3" +name = "charset-normalizer" +version = "2.0.7" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.5.0" + +[package.extras] +unicode_backport = ["unicodedata2"] [[package]] name = "colorama" @@ -109,22 +119,14 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] [[package]] name = "coverage" -version = "5.5" +version = "6.1.2" description = "Code coverage measurement for Python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" +python-versions = ">=3.6" [package.extras] -toml = ["toml"] - -[[package]] -name = "cython" -version = "0.29.23" -description = "The Cython compiler for writing C extensions for the Python language." -category = "main" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +toml = ["tomli"] [[package]] name = "dataclasses" @@ -136,7 +138,7 @@ python-versions = ">=3.6, <3.7" [[package]] name = "distlib" -version = "0.3.1" +version = "0.3.3" description = "Distribution utilities" category = "dev" optional = false @@ -160,11 +162,15 @@ python-versions = "*" [[package]] name = "filelock" -version = "3.0.12" +version = "3.3.2" description = "A platform independent file lock." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" + +[package.extras] +docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] +testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] [[package]] name = "flake8" @@ -193,15 +199,15 @@ flake8 = "*" [[package]] name = "idna" -version = "2.10" +version = "3.3" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.5" [[package]] name = "imagesize" -version = "1.2.0" +version = "1.3.0" description = "Getting image size from png/jpeg/jpeg2000/gif file" category = "main" optional = false @@ -209,7 +215,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.0.1" +version = "4.8.2" description = "Read metadata from Python packages" category = "dev" optional = false @@ -221,22 +227,23 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +perf = ["ipython"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "5.1.2" +version = "5.4.0" description = "Read resources from Python packages" category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -zipp = {version = ">=0.4", markers = "python_version < \"3.8\""} +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "pytest-black (>=0.3.7)", "pytest-mypy"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"] [[package]] name = "iniconfig" @@ -248,35 +255,34 @@ python-versions = "*" [[package]] name = "isort" -version = "4.3.21" +version = "5.8.0" description = "A Python utility / library to sort Python imports." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6,<4.0" [package.extras] -pipfile = ["pipreqs", "requirementslib"] -pyproject = ["toml"] -requirements = ["pipreqs", "pip-api"] -xdg_home = ["appdirs (>=1.4.0)"] +pipfile_deprecated_finder = ["pipreqs", "requirementslib"] +requirements_deprecated_finder = ["pipreqs", "pip-api"] +colors = ["colorama (>=0.4.3,<0.5.0)"] [[package]] name = "jinja2" -version = "2.11.3" +version = "3.0.3" description = "A very fast and expressive template engine." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [package.dependencies] -MarkupSafe = ">=0.23" +MarkupSafe = ">=2.0" [package.extras] -i18n = ["Babel (>=0.8)"] +i18n = ["Babel (>=2.7)"] [[package]] name = "joblib" -version = "1.0.1" +version = "1.1.0" description = "Lightweight pipelining with Python functions" category = "main" optional = true @@ -284,11 +290,11 @@ python-versions = ">=3.6" [[package]] name = "lazy-object-proxy" -version = "1.4.3" +version = "1.6.0" description = "A fast and thorough lazy object proxy." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [[package]] name = "markdown-it-py" @@ -311,11 +317,11 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", [[package]] name = "markupsafe" -version = "1.1.1" +version = "2.0.1" description = "Safely add untrusted strings to HTML/XML markup." category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=3.6" [[package]] name = "mccabe" @@ -354,7 +360,7 @@ scipy = "*" [[package]] name = "mdtraj" -version = "1.9.5" +version = "1.9.7" description = "MDTraj: A modern, open library for the analysis of molecular dynamics trajectories" category = "main" optional = false @@ -390,7 +396,15 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest [[package]] name = "numpy" -version = "1.20.2" +version = "1.19.5" +description = "NumPy is the fundamental package for array computing with Python." +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "numpy" +version = "1.21.1" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -398,11 +412,11 @@ python-versions = ">=3.7" [[package]] name = "packaging" -version = "20.9" +version = "21.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] pyparsing = ">=2.0.2" @@ -418,37 +432,49 @@ python-versions = "*" [package.dependencies] flake8-polyfill = ">=1.0.2,<2" +[[package]] +name = "platformdirs" +version = "2.4.0" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] + [[package]] name = "pluggy" -version = "0.13.1" +version = "1.0.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} [package.extras] dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "prospector" -version = "1.3.1" +version = "1.4.1.1" description = "Prospector: python static analysis tool" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" [package.dependencies] -astroid = "2.4.1" dodgy = ">=0.1.9" mccabe = ">=0.5.0" pep8-naming = ">=0.3.3,<=0.10.0" -pycodestyle = ">=2.6.0,<2.7.0" +pycodestyle = ">=2.6.0,<2.9.0" pydocstyle = ">=2.0.0" pyflakes = ">=2.2.0,<2.3.0" -pylint = "2.5.3" +pylint = ">=2.8.3,<3" pylint-celery = "0.3" pylint-django = "<2.2.0" pylint-flask = "0.6" @@ -467,11 +493,11 @@ with_vulture = ["vulture (>=1.5)"] [[package]] name = "py" -version = "1.10.0" +version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pycodestyle" @@ -483,7 +509,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydocstyle" -version = "6.0.0" +version = "6.1.1" description = "Python docstring style checker" category = "dev" optional = false @@ -492,6 +518,9 @@ python-versions = ">=3.6" [package.dependencies] snowballstemmer = "*" +[package.extras] +toml = ["toml"] + [[package]] name = "pyflakes" version = "2.2.0" @@ -502,7 +531,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.8.1" +version = "2.10.0" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false @@ -510,18 +539,20 @@ python-versions = ">=3.5" [[package]] name = "pylint" -version = "2.5.3" +version = "2.11.1" description = "python code static checker" category = "dev" optional = false -python-versions = ">=3.5.*" +python-versions = "~=3.6" [package.dependencies] -astroid = ">=2.4.0,<=2.5" +astroid = ">=2.8.0,<2.9" colorama = {version = "*", markers = "sys_platform == \"win32\""} -isort = ">=4.2.5,<5" +isort = ">=4.2.5,<6" mccabe = ">=0.6,<0.7" +platformdirs = ">=2.2.0" toml = ">=0.7.1" +typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""} [[package]] name = "pylint-celery" @@ -576,15 +607,18 @@ pylint = ">=1.7" [[package]] name = "pyparsing" -version = "2.4.7" +version = "3.0.6" description = "Python parsing module" category = "main" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +python-versions = ">=3.6" + +[package.extras] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" -version = "6.2.3" +version = "6.2.5" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -597,7 +631,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<1.0.0a1" +pluggy = ">=0.12,<2.0" py = ">=1.8.2" toml = "*" @@ -606,7 +640,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm [[package]] name = "pytest-cov" -version = "2.11.1" +version = "2.12.1" description = "Pytest plugin for measuring coverage." category = "dev" optional = false @@ -615,13 +649,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.dependencies] coverage = ">=5.2.1" pytest = ">=4.6" +toml = "*" [package.extras] -testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] [[package]] name = "pytz" -version = "2021.1" +version = "2021.3" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -629,29 +664,29 @@ python-versions = "*" [[package]] name = "pyyaml" -version = "5.4.1" +version = "6.0" description = "YAML parser and emitter for Python" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.6" [[package]] name = "requests" -version = "2.25.1" +version = "2.26.0" description = "Python HTTP for Humans." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<5" -idna = ">=2.5,<3" +charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} +idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} urllib3 = ">=1.21.1,<1.27" [package.extras] -security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] [[package]] name = "requirements-detector" @@ -695,7 +730,7 @@ docutils = ">=0.7" [[package]] name = "scikit-learn" -version = "0.24.1" +version = "0.24.2" description = "A set of python modules for machine learning and data mining" category = "main" optional = true @@ -726,18 +761,18 @@ numpy = ">=1.14.5" [[package]] name = "setoptconf" -version = "0.2.0" +version = "0.3.0" description = "A module for retrieving program settings from various sources in a consistant method." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.0" [package.extras] -YAML = ["pyyaml"] +yaml = ["pyyaml"] [[package]] name = "six" -version = "1.15.0" +version = "1.16.0" description = "Python 2 and 3 compatibility utilities" category = "main" optional = false @@ -784,14 +819,14 @@ test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] [[package]] name = "sphinx-autoapi" -version = "1.8.1" +version = "1.8.4" description = "Sphinx API documentation generator" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -astroid = ">=2.4" +astroid = ">=2.7" Jinja2 = "*" PyYAML = "*" sphinx = ">=3.0" @@ -843,11 +878,11 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "1.0.3" +version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] lint = ["flake8", "mypy", "docutils-stubs"] @@ -878,7 +913,7 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.4" +version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." category = "main" optional = false @@ -890,11 +925,11 @@ test = ["pytest"] [[package]] name = "threadpoolctl" -version = "2.1.0" +version = "3.0.0" description = "threadpoolctl" category = "main" optional = true -python-versions = ">=3.5" +python-versions = ">=3.6" [[package]] name = "toml" @@ -906,7 +941,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "tox" -version = "3.23.0" +version = "3.24.4" description = "tox is a generic virtualenv management and test command line tool" category = "dev" optional = false @@ -929,15 +964,15 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "psutil (>=5.6.1)", "pytes [[package]] name = "typed-ast" -version = "1.4.3" +version = "1.5.0" description = "a fork of Python 2 and 3 ast modules with type comment support" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "typing-extensions" -version = "3.7.4.3" +version = "3.10.0.2" description = "Backported and Experimental Type Hints for Python 3.5+" category = "main" optional = false @@ -945,44 +980,45 @@ python-versions = "*" [[package]] name = "unidecode" -version = "1.2.0" +version = "1.3.2" description = "ASCII transliterations of Unicode text" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.5" [[package]] name = "urllib3" -version = "1.26.4" +version = "1.26.7" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] +brotli = ["brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] -brotli = ["brotlipy (>=0.6.0)"] [[package]] name = "virtualenv" -version = "20.4.4" +version = "20.10.0" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [package.dependencies] -appdirs = ">=1.4.3,<2" +"backports.entry-points-selectable" = ">=1.0.4" distlib = ">=0.3.1,<1" -filelock = ">=3.0.0,<4" +filelock = ">=3.2,<4" importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} importlib-resources = {version = ">=1.0", markers = "python_version < \"3.7\""} +platformdirs = ">=2,<3" six = ">=1.9.0,<2" [package.extras] -docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=19.9.0rc1)"] -testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)", "xonsh (>=0.9.16)"] +docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"] +testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"] [[package]] name = "vulture" @@ -997,11 +1033,11 @@ toml = "*" [[package]] name = "wrapt" -version = "1.12.1" +version = "1.13.3" description = "Module for decorators, wrappers and monkey patching." category = "main" optional = false -python-versions = "*" 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